The proposed experiments are designed to examine the level, nature, organization and significance of naturally occurring DNA sequence variation in two large, well characterized regions of the Drosophila melanogaster genome (rosy-Ace region and Bithorax Complex). Four nested levels are proposed. The first involves examining three large samples of chromosomes from natural populations of D. melanogaster for DNA sequence variability using four six-base restriction endonucleases. The regions to be studied are the 315 kb rosy-Ace region of the third chromosome, and the nearby 400\kb Bithorax Complex. Questions to be addressed include: 1) Does a correlation exist between transcriptional activity of a region and the level of nucleotide and/or insertion/deletion polymorphism? 2) Is there evidence of insertional hotspots for transposable elements? 3) How is the variation at different genes along the sequence organized? Are nonrandom associations associated with clusters of functionally related genes? 4) Does the pattern of nonrandom association reflect variation in the rates of recombination through these regions? The second level of examination will be by four-base restriction analysis of the rosy locus. This approach will allow the examination of approximately 20% of the nucleotides in a 10 kb region in several hundred lines. The third level of the project will be to ask how variation at the DNA level is related to variation at the "phenotypic" level by quantitating levels of expression for rosy and Ace. Twenty lines of divergent haplotype, allozyme and activity will be selected for complete DNA sequencing of Xdh (level 4). These data will allow more refined answers to questions 1, 3 and 4 above as well as the contribution of intragenic recombination to allelic diversity segregating in natural populations.